or
or
By clicking below, you agree to our terms of service.
New to HackMD? Sign up
Syntax | Example | Reference | |
---|---|---|---|
# Header | Header | 基本排版 | |
- Unordered List |
|
||
1. Ordered List |
|
||
- [ ] Todo List |
|
||
> Blockquote | Blockquote |
||
**Bold font** | Bold font | ||
*Italics font* | Italics font | ||
~~Strikethrough~~ | |||
19^th^ | 19th | ||
H~2~O | H2O | ||
++Inserted text++ | Inserted text | ||
==Marked text== | Marked text | ||
[link text](https:// "title") | Link | ||
 | Image | ||
`Code` | Code |
在筆記中貼入程式碼 | |
```javascript var i = 0; ``` |
|
||
:smile: | ![]() |
Emoji list | |
{%youtube youtube_id %} | Externals | ||
$L^aT_eX$ | LaTeX | ||
:::info This is a alert area. ::: |
This is a alert area. |
On a scale of 0-10, how likely is it that you would recommend HackMD to your friends, family or business associates?
Please give us some advice and help us improve HackMD.
Syncing
xxxxxxxxxx
NeXML to JSON-LD conversion
original idea issue: https://github.com/phenoscape/KB-DataFest-2017/issues/27
Results
nexld
library for R, which can convert NexML to NexLD and back.Questions we can focus on
Derivative outcomes
Goal
Use cases
Deliverables
curl 'http://kb.phenoscape.org/api/ontotrace?taxon=%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVTO_0037519%3E&entity=%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000050%3E%20some%20%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0004765%3E&variable_only=true' -H 'Accept-Encoding: gzip, deflate' -H 'Connection: keep-alive' --compressed
Z * [ ] Example of an OpenTree NexSON files (not recommended for interoperability).
JSON-LD
changes to make to the nexld implementation
"@id": "VTO_0065870"
goes to"@id": "obo:VTO_0065870"
<– not necessary if a @vocab is set!@vocab
in@context
null
? or remove the key?spec
top level keys (are these okay, should they be changed?):
@context
[hash]TBD hash@vocab
obo:http://purl.obolibrary.org/obo/
)version
[string] (not needed if we don't use@vocab
)schemaLocation
[string] IRIs (optional?)otus
[array] each element is aotu
hashcharacters
[hash]@id
[IRI]trees
[hash]@id
[IRI]otus
[string]otus
hash (arbitrary set of keys): what OTUs do we have information about@type
@id
label
about
(Carl suggests to remove this) REMOVEdwc:taxonID
characters
hash: what characters do we define here?@id
@type
type
: another attribute for type of dataotus
REMOVEformat
states
char
matrix
(MOVE TOdata
HASH)seq
data
hash (wasmatrix
)*
trees
hash@id
otus
tree
node
edges
labels
context file
example (click to expand)
Gaurav's notes
Phenoscape and NeXML
Some data that's accessible from the Phenoscape RCN
/term/search
can look up taxonomic names, giving you a VTO term (e.g. http://purl.obolibrary.org/obo/VTO_0011993)/taxon
can give you a bunch of details about a taxon.Example NeXML files
Aligned vs unaligned data
We can also distinguish between cases where a character is homologous ("ratio of x to y") or non-homologous ("body_length").
Converting NeXML to CDAO
NeXML structure as per its XSD specification
* "tree=": xs:IDREFS
* "network=": xs:IDREFS
Matt's notes
temp - attributes
Framing spam